Zobrazeno 1 - 10
of 29
pro vyhledávání: '"Robert W. Cottingham"'
Autor:
Xiaohan Yang, June I. Medford, Kasey Markel, Patrick M. Shih, Henrique C. De Paoli, Cong T. Trinh, Alistair J. McCormick, Raphael Ployet, Steven G. Hussey, Alexander A. Myburg, Poul Erik Jensen, Md Mahmudul Hassan, Jin Zhang, Wellington Muchero, Udaya C. Kalluri, Hengfu Yin, Renying Zhuo, Paul E. Abraham, Jin-Gui Chen, David J. Weston, Yinong Yang, Degao Liu, Yi Li, Jessy Labbe, Bing Yang, Jun Hyung Lee, Robert W. Cottingham, Stanton Martin, Mengzhu Lu, Timothy J. Tschaplinski, Guoliang Yuan, Haiwei Lu, Priya Ranjan, Julie C. Mitchell, Stan D. Wullschleger, Gerald A. Tuskan
Publikováno v:
BioDesign Research, Vol 2020 (2020)
Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they ar
Externí odkaz:
https://doaj.org/article/24bf47722b144d758d6e3c016167a800
Biology is a quest; an ongoing inquiry about the nature of life. How do the different forms of life interact? What makes up an ecosystem? How does a tiny bacterium work? To answer these questions biologists turn increasingly to sophisticated computat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8cd5dd4aeb6fc3c2d9d39ac37fdb86f2
https://doi.org/10.1101/2022.12.20.521257
https://doi.org/10.1101/2022.12.20.521257
Autor:
Dylan Chivian, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Benjamin H. Allen, Mikayla M. Clark, Tianhao Gu, Miriam L. Land, Gavin A. Price, William J. Riehl, Michael W. Sneddon, Roman Sutormin, Qizhi Zhang, Robert W. Cottingham, Chris S. Henry, Adam P. Arkin
Publikováno v:
Nature Protocols.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ff4884c1371b3c44e75542abad4c1944
https://doi.org/10.1038/s41596-022-00794-4
https://doi.org/10.1038/s41596-022-00794-4
Autor:
Dylan, Chivian, Sean P, Jungbluth, Paramvir S, Dehal, Elisha M, Wood-Charlson, Richard S, Canon, Benjamin H, Allen, Mikayla M, Clark, Tianhao, Gu, Miriam L, Land, Gavin A, Price, William J, Riehl, Michael W, Sneddon, Roman, Sutormin, Qizhi, Zhang, Robert W, Cottingham, Chris S, Henry, Adam P, Arkin
Publikováno v:
Nature protocols.
Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. To realize the hope of capturing Earth's micr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::894d6877e8c1518ba141af01ebae2606
https://pubmed.ncbi.nlm.nih.gov/36451056
https://pubmed.ncbi.nlm.nih.gov/36451056
Autor:
Samuel M. D. Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, José P. Faria, Janaka N. Edirisinghe, Michael Mundy, Nicholas Chia, Elad Noor, Moritz E. Beber, Aaron A. Best, Matthew DeJongh, Jeffrey A. Kimbrel, Patrik D’haeseleer, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry
Introduction For over ten years, the ModelSEED has been a primary resource for researchers endeavoring to construct draft genome-scale metabolic models based on annotated microbial or plant genomes. As described here, and now being released, the Mode
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6e3a7cd19fc36108c16979fd576a6182
Autor:
Kasey Markel, Mahmudul Hassan, Renying Zhuo, Priya Ranjan, Jin Zhang, Yi Li, David J. Weston, Xiaohan Yang, Cong T. Trinh, Degao Liu, Guoliang Yuan, Gerald A. Tuskan, Wellington Muchero, Yinong Yang, Timothy J. Tschaplinski, Stanton L. Martin, Haiwei Lu, Bing Yang, Jessy Labbé, Stan D. Wullschleger, June I. Medford, Jun Hyung Lee, Udaya C. Kalluri, Raphael Ployet, Poul Erik Jensen, Alistair J. McCormick, Robert W. Cottingham, Hengfu Yin, Henrique Cestari De Paoli, Patrick M. Shih, Julie C. Mitchell, Alexander Andrew Myburg, Steven G. Hussey, Mengzhu Lu, Jin-Gui Chen, Paul E. Abraham
Publikováno v:
Yang, X, Medford, J I, Markel, K, Shih, P M, De Paoli, H C, Trinh, C T, McCormick, A J, Ployet, R, Hussey, S, Myburg, A A, Jensen, P E, Hassan, M M, Zhang, J, Muchero, W, Kalluri, U C, Hengfu, Y, Zhuo, R, Abraham, P E, Chen, J G, Weston, D J, Yang, Y, Liu, D, Li, Y, Labbe, J, Yang, B, Hyung Lee, J, Cottingham, R W, Martin, S, Lu, M, Tschaplinski, T J, Tschaplinski, T J, Yuan, G, Ranjan, P, Mitchell, J C, Wullschleger, S D & Tuskan, G A 2020, ' Plant biosystems design research roadmap 1.0 ', BioDesign Research . https://doi.org/10.34133/2020/8051764
Yang, X, Medford, J I, Markel, K, Shih, P M, De Paoli, H C, Trinh, C T, McCormick, A J, Ployet, R, Hussey, S G, Myburg, A A, Jensen, P E, Hassan, M M, Zhang, J, Muchero, W, Kalluri, U C, Yin, H, Zhuo, R, Abraham, P E, Chen, J-G, Weston, D J, Yang, Y, Liu, D, Li, Y, Labbe, J, Yang, B, Lee, J H, Cottingham, R W, Martin, S, Lu, M, Tschaplinski, T J, Yuan, G, Lu, H, Ranjan, P, Mitchell, J C, Wullschleger, S D & Tuskan, G A 2020, ' Plant Biosystems Design Research Roadmap 1.0 ', BioDesign Research, vol. 2020, 8051764 . https://doi.org/10.34133/2020/8051764
BioDesign Research, Vol 2020 (2020)
Yang, X, Medford, J I, Markel, K, Shih, P M, De Paoli, H C, Trinh, C T, McCormick, A J, Ployet, R, Hussey, S G, Myburg, A A, Jensen, P E, Hassan, M M, Zhang, J, Muchero, W, Kalluri, U C, Yin, H, Zhuo, R, Abraham, P E, Chen, J-G, Weston, D J, Yang, Y, Liu, D, Li, Y, Labbe, J, Yang, B, Lee, J H, Cottingham, R W, Martin, S, Lu, M, Tschaplinski, T J, Yuan, G, Lu, H, Ranjan, P, Mitchell, J C, Wullschleger, S D & Tuskan, G A 2020, ' Plant Biosystems Design Research Roadmap 1.0 ', BioDesign Research, vol. 2020, 8051764 . https://doi.org/10.34133/2020/8051764
BioDesign Research, Vol 2020 (2020)
Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they ar
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::55d05071243f65d4aff11e19484f6786
https://doi.org/10.34133/2020/8051764
https://doi.org/10.34133/2020/8051764
Autor:
Konstantinos Mavromatis, Miriam L Land, Thomas S Brettin, Daniel J Quest, Alex Copeland, Alicia Clum, Lynne Goodwin, Tanja Woyke, Alla Lapidus, Hans Peter Klenk, Robert W Cottingham, Nikos C Kyrpides
Publikováno v:
PLoS ONE, Vol 7, Iss 12, p e48837 (2012)
BackgroundThe emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled micro
Externí odkaz:
https://doaj.org/article/9b63d13f585d4aad871da6726ffa660e
Autor:
Shinjae Yoo, Matthew L. Henderson, Sarah S. Poon, Pavel S. Novichkov, Mark Mills, Roy T. Kamimura, Adam P. Arkin, Rick Stevens, Holly L. Haun, Shinnosuke Kondo, Meghan M Drake, Aaron A. Best, José P. Faria, Fernando Perez, Matthew DeJongh, Gang Fang, Thomas Brettin, Sergei Maslov, Janaka N. Edirisinghe, Folker Meyer, Jer Ming Chia, Scott Devoid, Doreen Ware, Steven E. Brenner, Paul M. Frybarger, Miriam Land, Dan Gunter, Fei He, John-Marc Chandonia, Hyunseung Yoo, Marcin P. Joachimiak, Dantong Yu, Christopher S. Henry, Mark Gerstein, Christopher Bun, Michael W. Sneddon, Samuel M. D. Seaver, Rashmi Jain, Stephen Y. Chan, Robert W. Cottingham, James J. Davis, Annette Greiner, Inna Dubchak, Vivek Kumar, Priya Ranjan, Daifeng Wang, Neal Conrad, James Thomason, Fangfang Xia, Maulik Shukla, Gavin Price, Nathan L. Tintle, Gary J. Olsen, Shiran Pasternak, Shane Canon, Roman A. Sutormin, William J. Riehl, Nomi L. Harris, Dan Murphy-Olson, Jason K. Baumohl, Wolfgang Gerlach, Benjamin H. Allen, Pamela C. Ronald, Michael C. Schatz, Mustafa H Syed, Brian H. Davison, Taeyun Oh, Dylan Chivian, Elizabeth M. Glass, R. L. Colasanti, Erik Pearson, David J. Weston, Sunita Kumari, Kevin P. Keegan, Emily M. Dietrich, Robert Olson, Srividya Ramakrishnan, James Gurtowski, Benjamin P. Bowen, Paramvir S. Dehal, Bruce Parrello
Publikováno v:
Nature biotechnology, vol 36, iss 7
Nature Biotechnology
Arkin, AP; Cottingham, RW; Henry, CS; Harris, NL; Stevens, RL; Maslov, S; et al.(2018). KBase: The United States department of energy systems biology knowledgebase. Nature Biotechnology, 36(7), 566-569. doi: 10.1038/nbt.4163. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/7p39r37f
Nature Biotechnology
Arkin, AP; Cottingham, RW; Henry, CS; Harris, NL; Stevens, RL; Maslov, S; et al.(2018). KBase: The United States department of energy systems biology knowledgebase. Nature Biotechnology, 36(7), 566-569. doi: 10.1038/nbt.4163. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/7p39r37f
Author(s): Arkin, Adam P; Cottingham, Robert W; Henry, Christopher S; Harris, Nomi L; Stevens, Rick L; Maslov, Sergei; Dehal, Paramvir; Ware, Doreen; Perez, Fernando; Canon, Shane; Sneddon, Michael W; Henderson, Matthew L; Riehl, William J; Murphy-Ol
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c789b3716f923398ce5518911fb65ab7
https://doi.org/10.1038/nbt.4163
https://doi.org/10.1038/nbt.4163
Autor:
Qizhi Zhang, Nicholas Chia, Michael B. Mundy, Patrik D'haeseleer, Christopher S. Henry, Aaron A. Best, Erik Pearson, Matthew DeJongh, Shane Canon, Janaka N. Edirisinghe, Filipe Liu, Robert W. Cottingham, Jeffrey A. Kimbrel, Moritz Emanuel Beber, José P. Faria, Elad Noor, Sean R. McCorkle, Samuel M. D. Seaver, Elisha M. Wood-Charlson, James G. Jeffryes, Adam P. Arkin, Jay R. Bolton
Publikováno v:
Nucleic Acids Research
Nucleic acids research, vol 49, iss D1
Seaver, S M D, Liu, F, Zhang, Q, Jeffryes, J, Faria, J P, Edirisinghe, J N, Mundy, M, Chia, N, Noor, E, Beber, M E, Best, A A, DeJongh, M, Kimbrel, J A, D'haeseleer, P, McCorkle, S R, Bolton, J R, Pearson, E, Canon, S, Wood-Charlson, E M, Cottingham, R W, Arkin, A P & Henry, C S 2021, ' The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes ', Nucleic Acids Research, vol. 49, no. D1, pp. D575–D588 . https://doi.org/10.1093/nar/gkaa746
Nucleic Acids Research, 49 (D1)
Nucleic acids research, vol 49, iss D1
Seaver, S M D, Liu, F, Zhang, Q, Jeffryes, J, Faria, J P, Edirisinghe, J N, Mundy, M, Chia, N, Noor, E, Beber, M E, Best, A A, DeJongh, M, Kimbrel, J A, D'haeseleer, P, McCorkle, S R, Bolton, J R, Pearson, E, Canon, S, Wood-Charlson, E M, Cottingham, R W, Arkin, A P & Henry, C S 2021, ' The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes ', Nucleic Acids Research, vol. 49, no. D1, pp. D575–D588 . https://doi.org/10.1093/nar/gkaa746
Nucleic Acids Research, 49 (D1)
For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3fd8a6e25516618d1c79a6007397d081
http://europepmc.org/articles/PMC7778962
http://europepmc.org/articles/PMC7778962
Publikováno v:
ASE
The bioinformatics software domain contains thousands of applications for automating tasks such as the pairwise alignment of DNA sequences, building and reasoning about metabolic models or simulating growth of an organism. Its end users range from so
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c00a1a4669e2bacc617db2bc1b931b5b
https://doi.org/10.1145/3238147.3240466
https://doi.org/10.1145/3238147.3240466